As part of a project to develop an integrated microfluidic biosensor for the detection of small molecules in saliva, practical issues of extraction of analytes from non-Newtonian samples using an H-filter were explored. The H-filter can be used to rapidly and efficiently extract small molecules from a complex sample into a simpler buffer. The location of the interface between the sample and buffer streams is a critical parameter in the function of the H-filter, so fluorescence microscopy was employed to monitor the interface position; this revealed apparently anomalous fluorophore diffusion from the samples into the buffer solutions. Using confocal microscopy to understand the three-dimensional distribution of the fluorophore, it was found that the interface between the non-Newtonian sample and Newtonian buffer was both curved and unstable. The core of the non-Newtonian sample extended into the Newtonian buffer and its position was unstable, producing a fluorescence intensity profile that gave rise to the apparently anomalously fast fluorophore transport. These instabilities resulted from the pairing of rheologically dissimilar fluid streams and were flowrate dependent. We conclude that use of non-Newtonian fluids, such as saliva, in the H-filter necessitates pretreatment to reduce viscoelasticity. The interfacial variation in position, stability and shape caused by the non-Newtonian samples has substantial implications for the use of biological samples for quantitative analysis and analyte extraction in concurrent flow extraction devices.